pacman::p_load(ggplot2, plotly, umap)

N=1e4
p = sqrt(2 + 2 * seq(-1, 1 - 2/N, 2/N))
d = data.frame(
  x = p * cos(2 * pi * p * 2), 
  y = 2 * runif(N, -1, 1), 
  z = p * sin(2 * pi * p * 2),
  color = seq(N) %/% 50
)

plotly::plot_ly(
  d, x = ~ x, y = ~ y, z = ~ z, color = ~ color, 
  type = "scatter3d", mode = "markers",
  marker = list(symbol = 'circle', sizemode = 'diameter', size = 2)
)

res <- umap::umap(d[-4])
res$layout %>%
  as.data.frame %>%
  setNames(c("umap_x", "umap_y")) %>%
  cbind(d) %>%
  ggplot(aes(umap_x, umap_y, color = color)) +
  geom_point() +
  scale_color_viridis_c()

3次元 -> 3次元にしてもあんまり意味はないけれど，やってみるとスイスロールがちょっとほどけた感じになる．

res <- umap::umap(d[-4], n_components = 3)
res$layout %>%
  as.data.frame %>%
  setNames(c("umap_x", "umap_y", "umap_z")) %>%
  cbind(d) %>%
  plotly::plot_ly(
  x = ~ umap_x, y = ~ umap_y, z = ~ umap_z, color = ~ color, 
  type = "scatter3d", mode = "markers",
  marker = list(symbol = 'circle', sizemode = 'diameter', size = 2)
)